How can I model indentations on a surface?
The secret is to model the indentations first, then use a deformer to create the twist.


Start with a cylinder with 9 sides.  Bevel (Ctrl + B) the edges and add an edge loop top and bottom, this will be the lip of the indentation.
Select the sides that will be indented.  Use polygon inset tool (I) to make them inset and indented.  





Add a Simple Deform modifier.  Adjust the angle to meet the reference image.





Add a Subdivision Surface modifier and preview the result.  Apply the deformation modifier.
Select top and bottom edge loops.  Use the LoopTools Circle tool (this requires the LoopTools addon).  





Extrude (E) the top and bottom faces and model the rest of the bottle.